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Adv."],"published-print":{"date-parts":[[2026,1,23]]},"abstract":"<jats:p>\n                    Mycobacterial granulomas lie at the center of tuberculosis (TB) pathogenesis and represent a unique niche where infecting bacteria survive under nutrient-restricted conditions and in the face of a host immune response. The granuloma\u2019s necrotic core, where bacteria reside extracellularly in humans, is difficult to assess in many experimentally tractable models. Here, using necrotic mycobacterial granulomas in adult zebrafish, we develop dual RNA sequencing (RNA-seq) across different host genotypes to identify the transcriptional alterations that enable bacteria to survive within this key microenvironment. Using pharmacological and genetic interventions, we find that neutrophils within mature, necrotic granulomas promote bacterial growth, in part through up-regulation of the bacterial\n                    <jats:italic toggle=\"yes\">devR<\/jats:italic>\n                    regulon. We identify conserved suites of bacterial transcriptional programs induced only in the context of this unique necrotic extracellular niche, including bacterial modules related to K\n                    <jats:sup>+<\/jats:sup>\n                    transport and\n                    <jats:italic toggle=\"yes\">rpf<\/jats:italic>\n                    genes. Analysis of\n                    <jats:italic toggle=\"yes\">Mycobacterium tuberculosis<\/jats:italic>\n                    strains across diverse lineages and human populations suggests that granuloma-specific transcriptional modules are targets for bacterial genetic adaptation in the context of human infection.\n                  <\/jats:p>","DOI":"10.1126\/sciadv.adw4619","type":"journal-article","created":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T19:00:26Z","timestamp":1769022026000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark","source":"Crossref","is-referenced-by-count":6,"title":["Granuloma dual RNA-seq reveals composite transcriptional programs driven by neutrophils and necrosis within tuberculous granulomas"],"prefix":"10.1126","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7027-1848","authenticated-orcid":true,"given":"Gopinath","family":"Viswanathan","sequence":"first","affiliation":[{"name":"Department of Molecular Genetics and 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27710, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8504-7518","authenticated-orcid":true,"given":"Jacob P.","family":"Lowy","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA."},{"name":"University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC 27710, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6355-0638","authenticated-orcid":true,"given":"Charlie J.","family":"Pyle","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Graham","family":"Alexander","sequence":"additional","affiliation":[{"name":"Sequencing and Genomics Technologies Core Facility, Duke University School of Medicine, Durham, NC 27710, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1910-8356","authenticated-orcid":true,"given":"Devjanee","family":"Swain-Lenz","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA."},{"name":"Sequencing and Genomics Technologies Core Facility, Duke University School of Medicine, Durham, NC 27710, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2284-5050","authenticated-orcid":true,"given":"Qingyun","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3465-5518","authenticated-orcid":true,"given":"David M.","family":"Tobin","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA."},{"name":"Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC 27710, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"221","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6976.2012.00331.x"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-immunol-032712-100022"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00281-015-0533-1"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-018-0215-8"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3009500"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2011.03.022"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2007.12.010"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1038\/nm.3412"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1301743"},{"key":"e_1_3_2_11_2","first-page":"956","article-title":"Early cellular reaction to tubercle 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